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- PDB-8qpl: F420-Dependent Methylene-Tetrahydromethanopterin Reductase with F... -

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Basic information

Entry
Database: PDB / ID: 8qpl
TitleF420-Dependent Methylene-Tetrahydromethanopterin Reductase with F420 from Methanocaldococcus jannaschii
Components5,10-methylenetetrahydromethanopterin reductase
KeywordsOXIDOREDUCTASE / F420-dependent methylene-tetrahydromethanopterin reductase / F420
Function / homology
Function and homology information


5,10-methylenetetrahydromethanopterin reductase / coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity / methanogenesis, from carbon dioxide / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / one-carbon metabolic process / cytoplasm
Similarity search - Function
5,10-methylenetetrahydromethanopterin reductase / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily
Similarity search - Domain/homology
COENZYME F420 / 5,10-methylenetetrahydromethanopterin reductase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGehl, M. / Demmer, U. / Ermler, U. / Shima, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Protein Sci. / Year: 2024
Title: Mutational and structural studies of ( beta alpha ) 8 -barrel fold methylene-tetrahydropterin reductases utilizing a common catalytic mechanism.
Authors: Gehl, M. / Demmer, U. / Ermler, U. / Shima, S.
History
DepositionOct 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5,10-methylenetetrahydromethanopterin reductase
B: 5,10-methylenetetrahydromethanopterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3354
Polymers70,7882
Non-polymers1,5472
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-3 kcal/mol
Surface area27740 Å2
Unit cell
Length a, b, c (Å)95.910, 95.910, 166.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-547-

HOH

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Components

#1: Protein 5,10-methylenetetrahydromethanopterin reductase


Mass: 35394.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: mer / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832SYB5
#2: Chemical ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H36N5O18P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 25% (v/v) polyethylene glycol monomethyl ether 550 100 mM MES pH 6.5 10 mM zinc sulfate 2 mM F420

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 60825 / % possible obs: 98.83 % / Redundancy: 1.902 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.31
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 1.63 / Num. unique obs: 8287 / CC1/2: 0.569

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.22 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 1998 3.28 %
Rwork0.2149 --
obs0.2163 60823 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→33.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4975 0 53 142 5170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145119
X-RAY DIFFRACTIONf_angle_d1.3256942
X-RAY DIFFRACTIONf_dihedral_angle_d8.925784
X-RAY DIFFRACTIONf_chiral_restr0.066800
X-RAY DIFFRACTIONf_plane_restr0.021884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.31621380.3164057X-RAY DIFFRACTION97
1.95-20.33851400.30844112X-RAY DIFFRACTION99
2-2.060.37141410.29154164X-RAY DIFFRACTION99
2.06-2.130.30171400.28244125X-RAY DIFFRACTION99
2.13-2.20.32451410.27444136X-RAY DIFFRACTION99
2.2-2.290.31031420.27494164X-RAY DIFFRACTION99
2.29-2.40.29911430.25314203X-RAY DIFFRACTION99
2.4-2.520.29511420.24914196X-RAY DIFFRACTION99
2.52-2.680.25841420.23954185X-RAY DIFFRACTION99
2.68-2.890.27271430.24134215X-RAY DIFFRACTION99
2.89-3.180.28771440.23954231X-RAY DIFFRACTION100
3.18-3.640.31011460.23494273X-RAY DIFFRACTION99
3.64-4.580.21471460.18454311X-RAY DIFFRACTION99
4.58-33.220.21771500.17564453X-RAY DIFFRACTION97

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